Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Modeling sub-threshold slope and DIBL mismatch of sub-22nm FinFet

A great challenge for future information technologies is building reliable systems on top of unreliable components. Parameters of modern and future technology devices are affected by severe levels of process variability and devices will degrade and even fail during the normal lifeDme of the chip due to aging mechanisms. These extreme levels of variability are caused by the high device miniaturizaDon and the random placement of individual atoms. Variability is considered a "red brick" by the InternaDonal Technology Roadmap for Semiconductors. The session is devoted to this topic presenDng research experiences from the Spanish Network on Variability called VARIABLES. In this session a talk entlited "Modeling sub-threshold slope and DIBL mismatch of sub-22nm FinFet" was presented.

Building a decision support system with a knowledge modeling tool

Knowledge modeling tools are software tools that follow a modeling approach to help developers in building a knowledge-based system. The purpose of this article is to show the advantages of using this type of tools in the development of complex knowledge-based decision support systems. In order to do so, the article describes the development of a system called SAIDA in the domain of hydrology with the help of the KSM modeling tool. SAIDA operates on real-time receiving data recorded by sensors (rainfall, water levels, flows, etc.). It follows a multi-agent architecture to interpret the data, predict the future behavior and recommend control actions. The system includes an advanced knowledge based architecture with multiple symbolic representation. KSM was especially useful to design and implement the complex knowledge based architecture in an efficient way.

Cross Ventilation CFD Modeling: Characterization and Study of Different Façade Openings Configurations at the Refurbishment of a Residential Building in Málaga (Spain)

The opening of new windows on the façade is proposed as a refurbishment strategy in an existing building in Málaga to facilitate cross ventilation of dwellings. The building is a residential block of 140 public housing units for rent for people with low income in Málaga (Spain), property of the City Council. By modeling with Computational Fluid Dynamics (CFD), eleven configurations of openings are studied in two different areas of the main housing type of the building. The quantity of introduced/extracted air into/from the room and the generated airflow patterns are obtained. The modeling allows comparing the different openings configurations to determine the most appropriate ventilation option for every room.

Inter-organizational information systems adoption for service innovation in building sector

The building sector has experienced a significant decline in recent years in Spain and Europe as a result of the financial crisis that began in 2007. This drop accompanies a low penetration of information and communication technologies in inter-organizational oriented business processes. The market decrease is causing a slowdown in the building sector, where only flexible small and medium enterprises (SMEs) survive thanks to specialization and innovation in services, which allow them to face new market demands. Inter-organizational information systems (IOISs) support innovation in services, and are thus a strategic tool for SMEs to obtain competitive advantage. Because of the inherent complexity of IOIS adoption, this research extends Kurnia and Johnston's (2000) theoretical model of IOIS adoption with an empirical model of IOIS characterization. The resultant model identifies the factors influencing IOIS adoption in SMEs in the building sector, to promote further service innovation for competitive and collaborative advantages. An empirical longitudinal study over six consecutive years using data from Spanish SMEs in the building sector validates the model, using the partial least squares technique and analyzing temporal stability. The main findings of this research are the four ways an IOIS might contribute to service innovation in the building sector. Namely: a) improving client interfaces and the link between service providers and end users; b) defining a specific market where SMEs can develop new service concepts; c) enhancing the service delivery system in traditional customer?supplier relationships; and d) introducing information and communication technologies and tools to improve information management.

Modeling construction time in Spanish building projects

The literature states that project duration is affected by various scope factors. Using 168 building projects carried out in Spain, this paper uses the multiple regression analysis to develop a forecast model that allows estimating project duration of new builds. The proposed model uses project type, gross floor area (GFA), the cost/GFA relationship and number of floors as predictor variables. The research identified the logarithmic form of construction speed as the most appropriate response variable. GFA has greater influence than cost on project duration but both factors are necessary to achieve a forecast model with the highest accuracy. We developed an analysis to verify the stability of forecasted values and showed how a model with high values of fit and accuracy may display an anomalous behavior in the forecasted values. The sensitivity of the proposed forecast model was also analyzed versus the variability of construction costs.

Architectural Technology and the BIM Acronym 3: Getting to Grips with BIM

Among Small and Medium Sized Enterprises (SMEs) in particular, the UK Government’s ambitions regarding BIM uptake and diffusion across the construction sector may be tempered by a realpolitik shaped in part by interactions between the industry, Higher Education (HE) and professional practice. That premise also has a global perspective. Building on the previous 2 papers, Architectural technology and the BIM Acronym 1 and 2, this third iteration is a synthesis of research and investigations carried out over a number of years directly related to the practical implementation of BIM and its impact upon BE SMEs. First challenges, risks and potential benefits for SMEs and micros in facing up to the necessity to engage with digital tools in a competitive and volatile marketplace are discussed including tailoring BIM to suit business models, and filtering out achievable BIM outcomes from generic and bespoke aspects of practice. Second the focus is on setting up and managing teams engaging with BIM scenarios, including the role of clients; addresses a range of paradigms including lonely BIM and collaborative working. The significance of taking a whole life view with BIM is investigated including embedding soft landings principles into project planning and realisation. Thirdly procedures for setting up and managing common data environments are identified and the value of achieving smooth information flow is addressed. The overall objective of this paper is to provide SMEs with a practical strategy to develop a toolkit to BIM implementation.

Boston, Massachusetts, 2-Dimensional Building Footprints with Height Data (from LIDAR data), 2002

This dataset consists of 2D footprints of the buildings in the metropolitan Boston area, based on tiles in the orthoimage index (orthophoto quad ID: 229890, 229894, 229898, 229902, 233886, 233890, 233894, 233898, 233902, 237890, 237894, 237898, 237902, 241890, 241894, 241898, 241902, 245898, 245902). This data set was collected using 3Di's Digital Airborne Topographic Imaging System II (DATIS II). Roof height and footprint elevation attributes (derived from 1-meter resolution LIDAR (LIght Detection And Ranging) data) are included as part of each building feature. This data can be combined with other datasets to create 3D representations of buildings and the surrounding environment.

Local information retrieval for the simulation and modeling system /

COO-1469-0174.

21st National Information Systems Security Conference : building the information security bridge to the 21st century : October 5-8, 1998, Hyatt Regency Crystal City, Arlington, Va.

Cover title.

Regional timber yield and cost information for the South : modeling techniques /

"October 1984."

Memorabilia of the city of Perth: containing, A guide to Perth; Historical memoranda repecting Perth; charters relating to the privileges of Perth; list of the ministers, and rectors of the grammar school and academy: list of the subscribers for building the bridge, and the public seminaries; and the Rev. Alexander Duff's (late of Tibbermuir) Traditional account, in the town of Perth, of the death of John, Earl of Gowrie, and his brother, Mr. Alexander Ruthven, in 1600. Compiled from the best sources of information; chiefly from Mr Cant's notes to The muse's threnodie of Adamson.

Added t.p., engraved.

Building rural America through farmers home insured notes : guaranteed by the full faith and credit of the United States of America : technical information for investors.

"Issued August 1969."

Building rural America through farmers home insured notes : guaranteed by the full faith and credit of the United States of America : technical information for investors.

"Issued August 1969, slightly revised December 1969."